Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 62 of 216
Found at i:18408541 original size:20 final size:20
Alignment explanation
Indices: 18408516--18408570 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
18408506 AATCTTATGC
18408516 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
*
18408536 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGGAATGGAAAG
18408556 TAAGTAAATGGAATG
1 TAAGTAAATGGAATG
18408571 TTATGTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGGAATGGAAAG
Found at i:18416200 original size:70 final size:70
Alignment explanation
Indices: 18416077--18416208 Score: 201
Period size: 70 Copynumber: 1.9 Consensus size: 70
18416067 TGGTTTGGCC
* *
18416077 GTGTTTCCCCTGTATCTTTAAAATTTCAAAACAGAATGTTCAAAATTATTCACACGACCTAGTAC
1 GTGTGTCCCCTGTATCTTTAAAATTTCAAAACAGAATGCTCAAAATTATTCACACGACCTAGTAC
18416142 TGGGT
66 TGGGT
* * * * *
18416147 GTGTGTCCCTTGTATCTTTCAAATTTCAAAATAGAATGCTCTAAATTATTCACACGGCCTAG
1 GTGTGTCCCCTGTATCTTTAAAATTTCAAAACAGAATGCTCAAAATTATTCACACGACCTAG
18416209 CACACGGGCA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 55 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (70 bp):
GTGTGTCCCCTGTATCTTTAAAATTTCAAAACAGAATGCTCAAAATTATTCACACGACCTAGTAC
TGGGT
Found at i:18431211 original size:25 final size:25
Alignment explanation
Indices: 18431183--18431238 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
18431173 CAGATCGCAT
* * *
18431183 GAGCTTAC-AGTTATTTAGCTCGGAG
1 GAGCTTACTA-TTATTCAACTCGAAG
18431208 GAGCTTACTATTATTCAACTCGAAG
1 GAGCTTACTATTATTCAACTCGAAG
18431233 GAGCTT
1 GAGCTT
18431239 GCCGTTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (25 bp):
GAGCTTACTATTATTCAACTCGAAG
Found at i:18431886 original size:122 final size:122
Alignment explanation
Indices: 18431731--18431950 Score: 431
Period size: 122 Copynumber: 1.8 Consensus size: 122
18431721 GAAAGCTTGT
18431731 CAGGTATTTAAATGAAACACACGAAAGTGATGTTACATGATACATTGATATATGAAATGAATAAT
1 CAGGTATTTAAATGAAACACACGAAAGTGATGTTACATGATACATTGATATATGAAATGAATAAT
18431796 ACATGTATATGAAATATGATTACTTGTTGAATTATATGAGTTCGATATGAACTATTA
66 ACATGTATATGAAATATGATTACTTGTTGAATTATATGAGTTCGATATGAACTATTA
*
18431853 CAGGTATTTAAATGAAACACACGAAAGTGATGTTACATGATGCATTGATATATGAAATGAATAAT
1 CAGGTATTTAAATGAAACACACGAAAGTGATGTTACATGATACATTGATATATGAAATGAATAAT
18431918 ACATGTATATGAAATATGATTACTTGTTGAATT
66 ACATGTATATGAAATATGATTACTTGTTGAATT
18431951 TGTCTATGTG
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 97 1.00
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (122 bp):
CAGGTATTTAAATGAAACACACGAAAGTGATGTTACATGATACATTGATATATGAAATGAATAAT
ACATGTATATGAAATATGATTACTTGTTGAATTATATGAGTTCGATATGAACTATTA
Found at i:18442127 original size:27 final size:27
Alignment explanation
Indices: 18442052--18442131 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 27
18442042 ATTGTAGAAC
*
18442052 AAGGTCTTGTGGTGAAACCATGGAGTT
1 AAGGTCTTGTGATGAAACCATGGAGTT
** * **
18442079 AAGG--AAGTGA--ATACC-TCTAGTT
1 AAGGTCTTGTGATGAAACCATGGAGTT
18442101 AAGGTCTTGTGATGAAACCATGGAGTT
1 AAGGTCTTGTGATGAAACCATGGAGTT
18442128 AAGG
1 AAGG
18442132 AGGCCACATG
Statistics
Matches: 37, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 9 0.24
23 4 0.11
24 4 0.11
25 3 0.08
26 4 0.11
27 13 0.35
ACGTcount: A:0.31, C:0.11, G:0.30, T:0.28
Consensus pattern (27 bp):
AAGGTCTTGTGATGAAACCATGGAGTT
Found at i:18444991 original size:41 final size:41
Alignment explanation
Indices: 18444930--18445086 Score: 172
Period size: 41 Copynumber: 3.8 Consensus size: 41
18444920 TGAAAATAAG
* * *
18444930 ATGTTTCAGACTTTACGTCTAGGAGGCTTGATGTCGATGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGATGAA
*
18444971 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGATGAA
* ** *
18445012 TTACTTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGC-TTGATGCCGATGAA
* * * * * *
18445053 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGC
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGC
18445087 TGGTGTTTTA
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
40 2 0.02
41 93 0.95
42 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (41 bp):
ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGATGAA
Found at i:18445075 original size:82 final size:82
Alignment explanation
Indices: 18444934--18445091 Score: 201
Period size: 82 Copynumber: 1.9 Consensus size: 82
18444924 AATAAGATGT
* * * *
18444934 TTCAGACTTTACGTCTAGGAGGCTTGATGTCGATGAAATGTTTCAGACTTTATGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGCT
18444999 TGATGCCGGTGAATTAC
66 TGATGCCGGTGAATTAC
* * * * *
18445016 TTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGTATCGGGCTTTGTGCCTAGCAGGC
1 TTCAGACTTTACGTCTAGCAGGC-TTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGC
* *
18445080 TTTATGCTGGTG
65 TTGATGCCGGTG
18445092 TTTTATACAA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
82 61 0.95
83 3 0.05
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.35
Consensus pattern (82 bp):
TTCAGACTTTACGTCTAGCAGGCTTGATGCCGATGAAATGTATCAGACTTTATGCCTAGCAGGCT
TGATGCCGGTGAATTAC
Found at i:18448226 original size:15 final size:14
Alignment explanation
Indices: 18448177--18448228 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
18448167 TATTTATTTA
18448177 TTAAAA-TATAT-T
1 TTAAAATTATATGT
18448189 TTAAAATTATAATGT
1 TTAAAATTAT-ATGT
*
18448204 ATAGAAATTATATGT
1 TTA-AAATTATATGT
18448219 TTGAAAATTA
1 TT-AAAATTA
18448229 AATCACTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 6 0.18
13 3 0.09
14 2 0.06
15 14 0.42
16 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (14 bp):
TTAAAATTATATGT
Found at i:18449077 original size:25 final size:25
Alignment explanation
Indices: 18449029--18449099 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
18449019 ATATTTAAAG
18449029 AGATAAATATATCGATTTATTTTAAATT
1 AGATAAATATA---ATTTATTTTAAATT
* *
18449057 AGATAAATATAATTTTTTTTACATT
1 AGATAAATATAATTTATTTTAAATT
*
18449082 -GAATAGATATAA-TTATTT
1 AG-ATAAATATAATTTATTT
18449100 CTATTTTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
24 6 0.16
25 21 0.55
28 11 0.29
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (25 bp):
AGATAAATATAATTTATTTTAAATT
Found at i:18449730 original size:14 final size:13
Alignment explanation
Indices: 18449703--18449728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18449693 AATTATGAGA
18449703 AAAATAATCATTT
1 AAAATAATCATTT
18449716 AAAATAATCATTT
1 AAAATAATCATTT
18449729 TATTATGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATAATCATTT
Found at i:18450113 original size:14 final size:13
Alignment explanation
Indices: 18450086--18450111 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18450076 AATTATGAGA
18450086 AAAATAATCATTT
1 AAAATAATCATTT
18450099 AAAATAATCATTT
1 AAAATAATCATTT
18450112 TATTATGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
AAAATAATCATTT
Found at i:18450580 original size:386 final size:383
Alignment explanation
Indices: 18449690--18450468 Score: 1242
Period size: 386 Copynumber: 2.0 Consensus size: 383
18449680 GTATATTTAA
* ** **
18449690 GGTAATTATGAGAAAAATAATCATTTAAAATAATCATTTTATTATGCAAATTTTGAGAAGAAATT
1 GGTAATCATGAGAAAAATAATCA--TAAAATAATCATTACATTATGCAAATTTTGAGAAGAAAGG
** * *
18449755 AAAATATTAATTAATTGAATT-AAAAA-T-AAAAAGATAATTTCTAATTAAAATTTTCGAAATAA
64 AAAATATTAACCAATTGAATTAAAAAACTAAAAAAGACAATTCCT-ATTAAAATTTTCGAAATAA
*
18449817 CTAAATGTAATTTATTATATAAAATTTTTTGAAAGAGTGATGAATTTTAGTATATATTCATATAT
128 CTAAATATAATTTATTATATAAAATTTTTTGAAAGAGTGATGAATTTTAGTATATATTCATATAT
* * *
18449882 GAAAATTATTATTTACAAAATCAATGTTGAACAATTTAAATAATACATTGTTTTTAGAATTGGAT
193 GAAAATTATTATTTACAAAATAAATGTTGAACAATTTAAATAATACATTGTTTTTAAAATTGAAT
18449947 TAGACAGATATATCGAAGATGGTCCACCCTATTTAATTAAAATTATAAAACTGTAAGAAAAGTGA
258 TAGACAGATATATCGAAGATGGTCCACCCTATTTAATTAAAATTATAAAACTGTAAGAAAAGTGA
*
18450012 TCGATCTAAAACTAGTGAACAATATTCCTATAGATTGAACCAGTACAAAAATGATATAACC
323 TCGATCTAAAACTAGTGAACAATATTCCTATAGAGTGAACCAGTACAAAAATGATATAACC
* ** **
18450073 GGTAATTATGAGAAAAATAATCATTTAAAATAATCATTTTATTATGCAAATTTTGAGAAGAAATT
1 GGTAATCATGAGAAAAATAATCA--TAAAATAATCATTACATTATGCAAATTTTGAGAAGAAAGG
** * *
18450138 AAAATATTAATTAATTGAATTAAAAAACTAAAAAAGATAATTTCTAATTAAAATTTTCGAAATAA
64 AAAATATTAACCAATTGAATTAAAAAACTAAAAAAGACAATTCCT-ATTAAAATTTTCGAAATAA
18450203 CTAAATATAATTTATTATATAAAATTTTTTGAAAGAGTGATGAATTTTAGTATATATTCATATAT
128 CTAAATATAATTTATTATATAAAATTTTTTGAAAGAGTGATGAATTTTAGTATATATTCATATAT
*
18450268 GAAAATTATTATTTACAAAATAAATGTTGAACAATTTAAATAATACCTTGTTTTTAAAATTGAAT
193 GAAAATTATTATTTACAAAATAAATGTTGAACAATTTAAATAATACATTGTTTTTAAAATTGAAT
18450333 TAGACAGATATATCGAAGATGGTCCACCCTATTTAATTAAAATTATAAAACTGTAAGAAAAGTGA
258 TAGACAGATATATCGAAGATGGTCCACCCTATTTAATTAAAATTATAAAACTGTAAGAAAAGTG-
*
18450398 ATCGATCTAAAATTAGTGAACAATATTCCTATAGAGTGAACCAGTACAAAAATGATATAACC
322 ATCGATCTAAAACTAGTGAACAATATTCCTATAGAGTGAACCAGTACAAAAATGATATAACC
18450460 GGT-ATCATG
1 GGTAATCATG
18450469 GAGGCCCTAT
Statistics
Matches: 384, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
383 86 0.22
384 5 0.01
385 1 0.00
386 229 0.60
387 63 0.16
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (383 bp):
GGTAATCATGAGAAAAATAATCATAAAATAATCATTACATTATGCAAATTTTGAGAAGAAAGGAA
AATATTAACCAATTGAATTAAAAAACTAAAAAAGACAATTCCTATTAAAATTTTCGAAATAACTA
AATATAATTTATTATATAAAATTTTTTGAAAGAGTGATGAATTTTAGTATATATTCATATATGAA
AATTATTATTTACAAAATAAATGTTGAACAATTTAAATAATACATTGTTTTTAAAATTGAATTAG
ACAGATATATCGAAGATGGTCCACCCTATTTAATTAAAATTATAAAACTGTAAGAAAAGTGATCG
ATCTAAAACTAGTGAACAATATTCCTATAGAGTGAACCAGTACAAAAATGATATAACC
Found at i:18451068 original size:10 final size:11
Alignment explanation
Indices: 18451024--18451070 Score: 53
Period size: 10 Copynumber: 4.3 Consensus size: 11
18451014 CATGCTTTTT
*
18451024 AAATAATTATAA
1 AAAT-ATTATTA
18451036 AAATATTA-TA
1 AAATATTATTA
18451046 AAATATTATTTA
1 AAATATTA-TTA
18451058 AAAT-TTATTA
1 AAATATTATTA
18451068 AAA
1 AAA
18451071 CTGACAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 15 0.47
11 7 0.22
12 10 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATATTATTA
Found at i:18466412 original size:20 final size:20
Alignment explanation
Indices: 18466389--18466436 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
18466379 GCGGCGTCGT
* *
18466389 AGTGCGAACAGAGACATCGA
1 AGTGCAAACAGAGACACCGA
*
18466409 AGTGCAAACAGAGGCACCGA
1 AGTGCAAACAGAGACACCGA
18466429 AGTGCAAA
1 AGTGCAAA
18466437 TCCCGTACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.42, C:0.21, G:0.29, T:0.08
Consensus pattern (20 bp):
AGTGCAAACAGAGACACCGA
Found at i:18466433 original size:40 final size:40
Alignment explanation
Indices: 18466330--18466436 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 40
18466320 GTATCAGAGA
* *
18466330 TGCATAACAGAGGTACCGAAGTGCAAATAGAGACATGAATG
1 TGCA-AACAGAGGCACCGAAGTGCAAACAGAGACATGAATG
* ** * *
18466371 TGCAAGA-AGCGGCGTCGTAGTGCGAACAGAGACATCGAA-G
1 TGCAA-ACAGAGGCACCGAAGTGCAAACAGAGACAT-GAATG
18466411 TGCAAACAGAGGCACCGAAGTGCAAA
1 TGCAAACAGAGGCACCGAAGTGCAAA
18466437 TCCCGTACAA
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
39 1 0.02
40 42 0.82
41 8 0.16
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.13
Consensus pattern (40 bp):
TGCAAACAGAGGCACCGAAGTGCAAACAGAGACATGAATG
Found at i:18470075 original size:21 final size:21
Alignment explanation
Indices: 18470049--18470088 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
18470039 AATTATCAAC
18470049 GAGTGGTACATCCATGACGGT
1 GAGTGGTACATCCATGACGGT
18470070 GAGTGGTACATCCATGACG
1 GAGTGGTACATCCATGACG
18470089 TGGTGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.23
Consensus pattern (21 bp):
GAGTGGTACATCCATGACGGT
Found at i:18472780 original size:21 final size:21
Alignment explanation
Indices: 18472756--18472802 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
18472746 GCCTAGTAAA
18472756 AAGTCTTGAGAACTTAGGTTC
1 AAGTCTTGAGAACTTAGGTTC
*
18472777 AAGTATTGAGAACTTAGGTTC
1 AAGTCTTGAGAACTTAGGTTC
18472798 AAGTC
1 AAGTC
18472803 ACATTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (21 bp):
AAGTCTTGAGAACTTAGGTTC
Found at i:18474502 original size:31 final size:31
Alignment explanation
Indices: 18474426--18474504 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
18474416 TACAATAAGC
*
18474426 CATCGTTGTCAGGCAACCCGGGGTGGCAGGT
1 CATCGTTGTCGGGCAACCCGGGGTGGCAGGT
* *
18474457 CATCGCTG-CTGGGCAACCCGGGGTGGCTGGT
1 CATCGTTGTC-GGGCAACCCGGGGTGGCAGGT
*
18474488 CATCATTGTCGGGCAAC
1 CATCGTTGTCGGGCAAC
18474505 TCAGGATGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 39 0.95
32 1 0.02
ACGTcount: A:0.15, C:0.28, G:0.37, T:0.20
Consensus pattern (31 bp):
CATCGTTGTCGGGCAACCCGGGGTGGCAGGT
Found at i:18509770 original size:17 final size:16
Alignment explanation
Indices: 18509745--18509778 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
18509735 TAGTTAATCT
*
18509745 TGTCGTTGCATTGTTAA
1 TGTCATTGCATT-TTAA
18509762 TGTCATTGCATTTTAA
1 TGTCATTGCATTTTAA
18509778 T
1 T
18509779 CTTAATGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.50
Consensus pattern (16 bp):
TGTCATTGCATTTTAA
Found at i:18511792 original size:39 final size:39
Alignment explanation
Indices: 18511738--18511812 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
18511728 TGCATTGGTA
*
18511738 GTGTATGCTTTCACATTAGTGCTATGACGTTAAACAGTC
1 GTGTATGCTTGCACATTAGTGCTATGACGTTAAACAGTC
* *
18511777 GTGTATGCTTGCACATTAGTGTTGTGACGTTAAACA
1 GTGTATGCTTGCACATTAGTGCTATGACGTTAAACA
18511813 ACCAATCAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (39 bp):
GTGTATGCTTGCACATTAGTGCTATGACGTTAAACAGTC
Found at i:18514906 original size:27 final size:27
Alignment explanation
Indices: 18514846--18514897 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
18514836 AATAGTCTGT
* *
18514846 CAAGACAGTAAACATGGGGTAGTCTAC
1 CAAGATAGTAAACATGGAGTAGTCTAC
18514873 CAAGATAGTAAACATGGAGTAGTCT
1 CAAGATAGTAAACATGGAGTAGTCT
18514898 GCTAGGATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.21
Consensus pattern (27 bp):
CAAGATAGTAAACATGGAGTAGTCTAC
Found at i:18514911 original size:27 final size:27
Alignment explanation
Indices: 18514854--18514911 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
18514844 GTCAAGACAG
* *
18514854 TAAACATGGGGTAGTCTACCAAGATAG
1 TAAACATGGAGTAGTCTACCAAGATAA
* * *
18514881 TAAACATGGAGTAGTCTGCTAGGATAA
1 TAAACATGGAGTAGTCTACCAAGATAA
18514908 TAAA
1 TAAA
18514912 TACGAGATAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (27 bp):
TAAACATGGAGTAGTCTACCAAGATAA
Found at i:18519997 original size:39 final size:40
Alignment explanation
Indices: 18519928--18520029 Score: 111
Period size: 41 Copynumber: 2.5 Consensus size: 40
18519918 TTAGTATAGA
* *
18519928 AGGCATGTTTCAACATGCAATCAGTTTAGTAG-A-AATAGTT
1 AGGCATGTTT-AACATGCAATCAGTATAGTAGCAGAACA-TT
*
18519968 -GGCATGTTTAACATGCAATTAGTAATAGTAGCAGAACATT
1 AGGCATGTTTAACATGCAATCAGT-ATAGTAGCAGAACATT
* *
18520008 AGGCATGCTTAACATGCGATCA
1 AGGCATGTTTAACATGCAATCA
18520030 ATTTCAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
38 13 0.25
39 15 0.29
40 3 0.06
41 21 0.40
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (40 bp):
AGGCATGTTTAACATGCAATCAGTATAGTAGCAGAACATT
Found at i:18523793 original size:19 final size:19
Alignment explanation
Indices: 18523760--18523815 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
18523750 TTTTTTTAAA
*
18523760 TATAAA-ATTTAGAATTTT
1 TATAAATATTTTGAATTTT
18523778 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
18523797 T-TAAATTATTTTGAATTTT
1 TATAAA-TATTTTGAATTTT
18523816 CTTTTTGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
18 10 0.29
19 25 0.71
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:18524712 original size:5 final size:5
Alignment explanation
Indices: 18524702--18524728 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
18524692 CATTGTGTAA
18524702 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
18524729 GTGACATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:18535236 original size:14 final size:14
Alignment explanation
Indices: 18535217--18535247 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
18535207 AAGGTATAAG
18535217 TGATTAATTCTCAC
1 TGATTAATTCTCAC
18535231 TGATTAATTCTCAC
1 TGATTAATTCTCAC
18535245 TGA
1 TGA
18535248 GTTTTTACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (14 bp):
TGATTAATTCTCAC
Found at i:18536445 original size:18 final size:18
Alignment explanation
Indices: 18536424--18536462 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
18536414 GTGAATTGTA
18536424 TTAATTTGGAAAACTTTG
1 TTAATTTGGAAAACTTTG
18536442 TTAATTTGGAAAACTTTG
1 TTAATTTGGAAAACTTTG
18536460 TTA
1 TTA
18536463 TTTATGCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.46
Consensus pattern (18 bp):
TTAATTTGGAAAACTTTG
Found at i:18542771 original size:21 final size:19
Alignment explanation
Indices: 18542739--18542782 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
18542729 GATGTAGTTC
18542739 AAAAAATTTTAAAAATTATT
1 AAAAAATTTTAAAAATTA-T
* *
18542759 AAAAAGTTGTTAAATATTAT
1 AAAAAATT-TTAAAAATTAT
18542779 AAAA
1 AAAA
18542783 TGATTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAAAATTTTAAAAATTAT
Found at i:18542782 original size:29 final size:28
Alignment explanation
Indices: 18542742--18542815 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 28
18542732 GTAGTTCAAA
*
18542742 AAATTTTA-AAAATTATTA-AAAAGTTGTT
1 AAATATTATAAAATTATTATAAAA-TTG-T
*
18542770 AAATATTATAAAATGATTATAAAATTGT
1 AAATATTATAAAATTATTATAAAATTGT
18542798 -AATAATTATAATAATTAT
1 AAAT-ATTATAA-AATTAT
18542816 CGATAATTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 3 0.08
28 15 0.38
29 17 0.44
30 4 0.10
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (28 bp):
AAATATTATAAAATTATTATAAAATTGT
Found at i:18542888 original size:19 final size:19
Alignment explanation
Indices: 18542865--18542914 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
18542855 TAAAAATGCT
18542865 ATAAAATGTTA-AAATATA
1 ATAAAATGTTATAAATATA
* *
18542883 AGTAAAGTATTATAAATATA
1 A-TAAAATGTTATAAATATA
*
18542903 ATAAAAAGTTAT
1 ATAAAATGTTAT
18542915 TCAAATTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 1 0.04
19 16 0.64
20 8 0.32
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (19 bp):
ATAAAATGTTATAAATATA
Found at i:18543210 original size:21 final size:22
Alignment explanation
Indices: 18543186--18543252 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 22
18543176 CTTTAAGTTT
* *
18543186 AATTTAAT-TTTCATATCATTA
1 AATTTAATATATCACATCATTA
18543207 AA-TTAATATATCACATCATTA
1 AATTTAATATATCACATCATTA
*
18543228 TATTT--TATAT-A-ATCATTA
1 AATTTAATATATCACATCATTA
*
18543246 ATTTTAA
1 AATTTAA
18543253 ATTTTATAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
18 10 0.27
19 1 0.03
20 10 0.27
21 14 0.38
22 2 0.05
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTAATATATCACATCATTA
Found at i:18544112 original size:16 final size:18
Alignment explanation
Indices: 18544093--18544125 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18544083 TTACATTTTG
18544093 ATAAG-TTTAAA-AAAAA
1 ATAAGATTTAAATAAAAA
18544109 ATAAGATTTAAATAAAA
1 ATAAGATTTAAATAAAA
18544126 GTTATCACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (18 bp):
ATAAGATTTAAATAAAAA
Found at i:18544640 original size:15 final size:17
Alignment explanation
Indices: 18544620--18544654 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
18544610 GGATCAAATT
18544620 AAAAA-AAAAAAGAAGA
1 AAAAACAAAAAAGAAGA
18544636 AAAAAGCAAAAAAGAAGA
1 AAAAA-CAAAAAAGAAGA
18544654 A
1 A
18544655 GATGAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
18 12 0.71
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAAGAAGA
Found at i:18550255 original size:13 final size:15
Alignment explanation
Indices: 18550234--18550265 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18550224 TGACAAAATC
*
18550234 AAAATATATTTTAAA
1 AAAATATATGTTAAA
18550249 AAAATATATGTTAAA
1 AAAATATATGTTAAA
18550264 AA
1 AA
18550266 TGCTAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATATATGTTAAA
Found at i:18550746 original size:3 final size:3
Alignment explanation
Indices: 18550717--18550777 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
18550707 ATAAATAAGT
*
18550717 ATA ATA ATT ATA ATA TATA AT- ATA ATA ATA A-A A-A ACTA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA
18550761 ATA CAGTA ATA ATA ATA
1 ATA -A-TA ATA ATA ATA
18550778 TAAATAAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
2 6 0.12
3 35 0.70
4 7 0.14
5 2 0.04
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18550776 original size:14 final size:14
Alignment explanation
Indices: 18550726--18550777 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
18550716 TATAATAATT
18550726 ATAATATATAATA-TA
1 ATAATA-ATAA-ACTA
*
18550741 ATAATAAAAAACTA
1 ATAATAATAAACTA
* *
18550755 ATAATAATACAGTA
1 ATAATAATAAACTA
18550769 ATAATAATA
1 ATAATAATA
18550778 TAAATAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 1 0.03
14 25 0.78
15 6 0.19
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (14 bp):
ATAATAATAAACTA
Found at i:18550780 original size:22 final size:21
Alignment explanation
Indices: 18550755--18550806 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
18550745 TAAAAAACTA
* *
18550755 ATAATAATACAGTAATAATAAT
1 ATAATAA-ACAGTAATAACAAC
*
18550777 ATAAATAAACAGTATTAACAAC
1 AT-AATAAACAGTAATAACAAC
18550799 ATAATAAA
1 ATAATAAA
18550807 AAACTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.23
22 15 0.58
23 5 0.19
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAATAAACAGTAATAACAAC
Found at i:18552264 original size:127 final size:126
Alignment explanation
Indices: 18552032--18552266 Score: 328
Period size: 127 Copynumber: 1.9 Consensus size: 126
18552022 AAGATAAGTC
* * * *
18552032 TGATGCGATCTGCTCTCTGCAATCTCAAAGAGATAAGATCTGATTTTAATCCGCTCCACTGCAAC
1 TGATGCGATCTACTCTCTGCAACCTCAAAGAGATAAGATCTGATGTTAATCCGCTCCACTACAAC
* * * *
18552097 TTCAGGGAGATAGGATTATTGGCTTCAGTCTGCTCCACTGCAACTTCAGGGAGTTAAGACT
66 TTCAGAGAGATAGGATTATTGACTTCAATCTGCTCAACTGCAACTTCAGGGAGTTAAGACT
*
18552158 TGATGCGATCTACTCTCTGCAACCTCGGAA-AGATAAGATCTGGATGTTAATCCGCTCCACTACA
1 TGATGCGATCTACTCTCTGCAACCTC-AAAGAGATAAGATCT-GATGTTAATCCGCTCCACTACA
* * * *
18552222 ACTTCAGAGAGATAGGATTATTTACTTCAATTTGTTTAACTGCAA
64 ACTTCAGAGAGATAGGATTATTGACTTCAATCTGCTCAACTGCAA
18552267 TGTAGGGGAA
Statistics
Matches: 94, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
126 35 0.37
127 59 0.63
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (126 bp):
TGATGCGATCTACTCTCTGCAACCTCAAAGAGATAAGATCTGATGTTAATCCGCTCCACTACAAC
TTCAGAGAGATAGGATTATTGACTTCAATCTGCTCAACTGCAACTTCAGGGAGTTAAGACT
Found at i:18552672 original size:88 final size:88
Alignment explanation
Indices: 18552553--18552727 Score: 226
Period size: 88 Copynumber: 2.0 Consensus size: 88
18552543 GATAAGACTG
* * ** *
18552553 GTATCTTCGATCTGCTTCGCTGCCAGTACAGGAA-AGTAAGATCTACCATTTTCAACCTACTCCA
1 GTATCTTCGATCTACTTCGCTACCAAAACAGGAAGA-CAAGATCTACCATTTTCAACCTACTCCA
18552617 CTGCTGCCCAAGGAGACAAGGCTA
65 CTGCTGCCCAAGGAGACAAGGCTA
* * * *
18552641 GTATCTTCGATCTACTTCGCTATCAAAACAGGAAGACAAGATCTGCTATTTTCAACCTACTCTAC
1 GTATCTTCGATCTACTTCGCTACCAAAACAGGAAGACAAGATCTACCATTTTCAACCTACTCCAC
* * *
18552706 TGCTGCTCAGGGAGATAAGGCT
66 TGCTGCCCAAGGAGACAAGGCT
18552728 GAAGTTTAAC
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
88 73 0.99
89 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (88 bp):
GTATCTTCGATCTACTTCGCTACCAAAACAGGAAGACAAGATCTACCATTTTCAACCTACTCCAC
TGCTGCCCAAGGAGACAAGGCTA
Found at i:18557292 original size:23 final size:24
Alignment explanation
Indices: 18557258--18557311 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
18557248 TGAACAAAAT
*
18557258 ATGATTATG-AAATCAATAAAAGA
1 ATGATTATGAAAAACAATAAAAGA
*
18557281 ATGATGTA-GAAAAAGAATAAAAGA
1 ATGAT-TATGAAAAACAATAAAAGA
*
18557305 ATAATTA
1 ATGATTA
18557312 CTCAAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.31
24 18 0.69
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (24 bp):
ATGATTATGAAAAACAATAAAAGA
Found at i:18557341 original size:26 final size:26
Alignment explanation
Indices: 18557290--18557345 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
18557280 AATGATGTAG
*
18557290 AAAAAGAATAAAAGAATAATTACTCA
1 AAAAAGAATAAAAGAATAATGACTCA
* * *
18557316 AAAAAGAATGAAAGAATACTGGCTCA
1 AAAAAGAATAAAAGAATAATGACTCA
18557342 AAAA
1 AAAA
18557346 TGCATACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.16
Consensus pattern (26 bp):
AAAAAGAATAAAAGAATAATGACTCA
Found at i:18564445 original size:13 final size:15
Alignment explanation
Indices: 18564424--18564455 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18564414 TCACAAAATC
*
18564424 AAAATATATTTTAAA
1 AAAATATATGTTAAA
18564439 AAAATATATGTTAAA
1 AAAATATATGTTAAA
18564454 AA
1 AA
18564456 TGTTCATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (15 bp):
AAAATATATGTTAAA
Found at i:18564933 original size:14 final size:13
Alignment explanation
Indices: 18564901--18564982 Score: 71
Period size: 14 Copynumber: 6.2 Consensus size: 13
18564891 CGCATATATA
18564901 AATAAGTATAATAAT
1 AATAA-TAT-ATAAT
*
18564916 TATAATATATAAT
1 AATAATATATAAT
18564929 ATATAATATAATAAT
1 A-ATAATAT-ATAAT
*
18564944 AATAA-A-CTAAT
1 AATAATATATAAT
*
18564955 AATAATACAGTAAT
1 AATAATATA-TAAT
18564969 AATAATATA-AAT
1 AATAATATATAAT
18564981 AA
1 AA
18564983 ATAGTATTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
11 9 0.16
12 6 0.11
13 6 0.11
14 26 0.46
15 10 0.18
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (13 bp):
AATAATATATAAT
Found at i:18564939 original size:25 final size:25
Alignment explanation
Indices: 18564911--18565002 Score: 77
Period size: 25 Copynumber: 3.8 Consensus size: 25
18564901 AATAAGTATA
*
18564911 ATAATTATAATATATAATATATAAT
1 ATAATAATAATATATAATATATAAT
*
18564936 ATAATAATAATAAACTAATA-ATAAT
1 ATAATAATAATATA-TAATATATAAT
* *
18564961 ACAGTAATAATAATATAA-ATA-AAT
1 ATAATAATAAT-ATATAATATATAAT
*
18564985 AGTATTAA-AA-ATATAATA
1 A-TAATAATAATATATAATA
18565003 AAAAACTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
22 6 0.11
23 1 0.02
24 7 0.13
25 34 0.62
26 7 0.13
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
ATAATAATAATATATAATATATAAT
Found at i:18564944 original size:3 final size:3
Alignment explanation
Indices: 18564908--18564975 Score: 68
Period size: 3 Copynumber: 22.0 Consensus size: 3
18564898 ATAAATAAGT
* *
18564908 ATA ATA ATT ATA ATA TATA ATA TATA AT- ATA ATA ATA ATA A-A CTA
1 ATA ATA ATA ATA ATA -ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
18564953 ATA ATA ATA CAGTA ATA ATA ATA
1 ATA ATA ATA -A-TA ATA ATA ATA
18564976 TAAATAAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
2 3 0.05
3 42 0.76
4 8 0.15
5 2 0.04
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:18568458 original size:48 final size:48
Alignment explanation
Indices: 18568387--18568481 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
18568377 TTCTTTGCTC
* **
18568387 AAAAACGCCTAAGTCAGCCTAACTTGCAGTAATAAAGGATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGGATTCAACAGT
* *
18568435 AAAAACGCCTAAGTCAGCTTAACTCGTAACAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGGATTCAACAG
18568482 AATTCCCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGGATTCAACAGT
Found at i:18568825 original size:36 final size:35
Alignment explanation
Indices: 18568780--18568850 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
18568770 CTAAGATCAT
*
18568780 ATATCTCAAAAGATCACCTTCCATATTTGCCAAGC
1 ATATCTCAAAAGATCACCTTCCATATTTCCCAAGC
* * *
18568815 ATATCTTCAAAAGATCTCTTTCCTTATTTCCCAAGC
1 ATATC-TCAAAAGATCACCTTCCATATTTCCCAAGC
18568851 TCCGGAGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 5 0.16
36 26 0.84
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (35 bp):
ATATCTCAAAAGATCACCTTCCATATTTCCCAAGC
Found at i:18573517 original size:48 final size:48
Alignment explanation
Indices: 18573446--18573540 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
18573436 TTCTTTACTA
* *
18573446 AAAAACGCCTAAGTCAGCCTAACTTGCAATAATAAAGGATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGGATTCAACAGT
*
18573494 AAAAACGCCTAAGTCAGCTTAACTCGCAACAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGGATTCAACAG
18573541 AATTCCCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.44, C:0.22, G:0.15, T:0.19
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGGATTCAACAGT
Found at i:18573878 original size:35 final size:36
Alignment explanation
Indices: 18573838--18573909 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
18573828 TCTAGGATCA
*
18573838 CATATC-TCAAAAGATCACCTTCCATATTTGCGAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
* * *
18573873 CATATCTTCAAAAGATCTCTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
18573909 C
1 C
18573910 TCCGGAGATG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 6 0.19
36 26 0.81
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
Found at i:18579300 original size:52 final size:51
Alignment explanation
Indices: 18579188--18579310 Score: 142
Period size: 52 Copynumber: 2.4 Consensus size: 51
18579178 TTCCTCAATT
* *
18579188 GAAAATATGCTGAAAATATTTTCTGCAAAAGTCAGATGATTTCCCACAACC
1 GAAAATATTCTGAAAATATTTTCTGCAAAAGTCAGAAGATTTCCCACAACC
* * * *
18579239 GAAAATATTCTGAAAAATATTTTCTGTAACAGTCA-AAGAATTTTCCATAA-C
1 GAAAATATTCTG-AAAATATTTTCTGCAAAAGTCAGAAG-ATTTCCCACAACC
*
18579290 TAAAAGTATTCTGAAAATATT
1 GAAAA-TATTCTGAAAATATT
18579311 CTTTTACATT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
51 26 0.42
52 36 0.58
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (51 bp):
GAAAATATTCTGAAAATATTTTCTGCAAAAGTCAGAAGATTTCCCACAACC
Found at i:18580049 original size:29 final size:29
Alignment explanation
Indices: 18580017--18580076 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
18580007 TTATTTATAT
18580017 TTTCAATTGTAACT-ATTTAATTTTTAAAG
1 TTTCAATTGTAA-TGATTTAATTTTTAAAG
18580046 TTTCAATTGTAATGATTTAATTTTTAAAG
1 TTTCAATTGTAATGATTTAATTTTTAAAG
18580075 TT
1 TT
18580077 AAATTTATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.53
Consensus pattern (29 bp):
TTTCAATTGTAATGATTTAATTTTTAAAG
Found at i:18587114 original size:24 final size:24
Alignment explanation
Indices: 18587087--18587145 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
18587077 TTATATGATA
18587087 TGAATATAATATGACAAAATTTAT
1 TGAATATAATATGACAAAATTTAT
** *
18587111 TGAA-ATATATATGTTAAATTTTAT
1 TGAATATA-ATATGACAAAATTTAT
*
18587135 T-TATATAATAT
1 TGAATATAATAT
18587146 ATAATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 8 0.28
24 21 0.72
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (24 bp):
TGAATATAATATGACAAAATTTAT
Found at i:18588198 original size:22 final size:22
Alignment explanation
Indices: 18588170--18588211 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
18588160 TCGGCCTTGG
18588170 GGCCTCTGGTGCTGACATTCCC
1 GGCCTCTGGTGCTGACATTCCC
*
18588192 GGCCTCTGGTGTTGACATTC
1 GGCCTCTGGTGCTGACATTC
18588212 TTTACACGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.31, G:0.29, T:0.31
Consensus pattern (22 bp):
GGCCTCTGGTGCTGACATTCCC
Found at i:18589650 original size:14 final size:14
Alignment explanation
Indices: 18589631--18589666 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
18589621 CTCTTTGCAT
*
18589631 ACAGAATATAAAAG
1 ACAGAATAAAAAAG
18589645 ACAGAATAAAAAAG
1 ACAGAATAAAAAAG
*
18589659 ACATAATA
1 ACAGAATA
18589667 GTGAAATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.67, C:0.08, G:0.11, T:0.14
Consensus pattern (14 bp):
ACAGAATAAAAAAG
Found at i:18592876 original size:18 final size:18
Alignment explanation
Indices: 18592845--18592882 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
18592835 AAAAAATAAC
*
18592845 ATTTTTTACATTTAATAT
1 ATTTTTTACATTTAAAAT
18592863 ATTTTTTA-ATTTTAAAAT
1 ATTTTTTACA-TTTAAAAT
18592881 AT
1 AT
18592883 ATCGTGCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTTTACATTTAAAAT
Found at i:18593027 original size:19 final size:19
Alignment explanation
Indices: 18592991--18593027 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18592981 AGTTAATAAT
*
18592991 AAATTTGATTATGGTGGGC
1 AAATTTGATTACGGTGGGC
*
18593010 AAATTTGATTACGTTGGG
1 AAATTTGATTACGGTGGG
18593028 TGATAGTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.05, G:0.30, T:0.38
Consensus pattern (19 bp):
AAATTTGATTACGGTGGGC
Found at i:18605524 original size:23 final size:23
Alignment explanation
Indices: 18605497--18605541 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
18605487 TTCAATATCA
*
18605497 TTCATAT-AATTTAATCATCATAT
1 TTCATATGAATGTAATC-TCATAT
*
18605520 TTCATTTGAATGTAATCTCATA
1 TTCATATGAATGTAATCTCATA
18605542 ACAATTTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (23 bp):
TTCATATGAATGTAATCTCATAT
Found at i:18605680 original size:20 final size:20
Alignment explanation
Indices: 18605652--18606077 Score: 402
Period size: 20 Copynumber: 21.3 Consensus size: 20
18605642 CATAGTGCTG
*
18605652 AACAAAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* * * *
18605672 TATAAAGGCACTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* ** * *
18605692 AATAGAGGTGCTGGAGTGCA
1 AACAGAGGCACCGAAGTGCA
* * *
18605712 AACAGAGACATCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
* * *
18605732 AATAGAGGCACCGGAGTGAA
1 AACAGAGGCACCGAAGTGCA
*
18605752 AACAAAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
18605772 AACAAAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
* *
18605792 TACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
*
18605812 AACAGAGGCACTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* **
18605832 TACAGAGGCATTGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
18605852 TACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
18605872 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
18605892 TACAGAGGCATCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* ** * *
18605912 TACAGAGATATCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
* *
18605932 AATAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
*
18605952 AACAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
18605972 AACAGAGGCACCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* *
18605992 TACAGAGGCATCGAAGTGCA
1 AACAGAGGCACCGAAGTGCA
* * *
18606012 TACAGAGGCACCAAACTGCA
1 AACAGAGGCACCGAAGTGCA
* * * ** *
18606032 AATAAAGGCATCGTGGTACA
1 AACAGAGGCACCGAAGTGCA
* *
18606052 AATAGAGGCACCGAAGTACA
1 AACAGAGGCACCGAAGTGCA
18606072 AACAGA
1 AACAGA
18606078 TACATTTCAA
Statistics
Matches: 336, Mismatches: 70, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 336 1.00
ACGTcount: A:0.42, C:0.21, G:0.27, T:0.11
Consensus pattern (20 bp):
AACAGAGGCACCGAAGTGCA
Found at i:18608622 original size:12 final size:12
Alignment explanation
Indices: 18608584--18608622 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
18608574 ACTAAAATGA
18608584 TTTAATAAAATT
1 TTTAATAAAATT
*
18608596 CTTAATAACATATT
1 TTTAATAA-A-ATT
18608610 TTTAATAAAATT
1 TTTAATAAAATT
18608622 T
1 T
18608623 CTAAATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 11 0.48
13 2 0.09
14 10 0.43
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (12 bp):
TTTAATAAAATT
Found at i:18608870 original size:21 final size:21
Alignment explanation
Indices: 18608829--18608870 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
18608819 AAGTTGATAG
**
18608829 TTTTTAATTTTGAAGTTTTTT
1 TTTTTAATTTTGAAGAATTTT
18608850 TTTTTAAATTTTGAA-AATTTT
1 TTTTT-AATTTTGAAGAATTTT
18608871 AATTTTCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTTTAATTTTGAAGAATTTT
Found at i:18608870 original size:22 final size:21
Alignment explanation
Indices: 18608829--18608870 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
18608819 AAGTTGATAG
**
18608829 TTTTTAATTTTGAAGTTTTTT
1 TTTTTAATTTTGAAAATTTTT
18608850 TTTTTAAATTTTGAAAATTTT
1 TTTTT-AATTTTGAAAATTTT
18608871 AATTTTCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTTTAATTTTGAAAATTTTT
Found at i:18608872 original size:16 final size:17
Alignment explanation
Indices: 18608851--18608888 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
18608841 AAGTTTTTTT
18608851 TTTTAAATTT-TGAAAA
1 TTTTAAATTTCTGAAAA
* *
18608867 TTTTAATTTTCTGAAAT
1 TTTTAAATTTCTGAAAA
18608884 TTTTA
1 TTTTA
18608889 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTTAAATTTCTGAAAA
Found at i:18615158 original size:124 final size:125
Alignment explanation
Indices: 18614847--18615198 Score: 521
Period size: 126 Copynumber: 2.8 Consensus size: 125
18614837 TAATTTCGAG
** * *
18614847 TTGACGTTTCTGATAAAATAGTATAAAATCGCTTCTAGCAGGATTCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTG
*
18614912 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTGCACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAA-TATTTTT
* *
18614973 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGTAGGATGCTATTTGTGAATAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTG
* * * *
18615038 AAATCGCGGCCTCGT-CA-GCAAGCTTTTGCTATAGTAGGTCATGTAAGAAATAA-ATTTTT
66 AAATCGCGCCCTCGTGCACGC--GCTTTTGCTACAGTAGGTCACGGAAGAAATAATATTTTT
*
18615097 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTG
* * *
18615162 AAATCGTGCCCTCGTGGATGCGCTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGCACGCGCTTTTGCTACAGTAG
18615199 CATGTTTGGG
Statistics
Matches: 204, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
124 98 0.48
125 2 0.01
126 104 0.51
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGCACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATATTTTT
Found at i:18618439 original size:116 final size:116
Alignment explanation
Indices: 18618230--18618572 Score: 616
Period size: 116 Copynumber: 3.0 Consensus size: 116
18618220 TGATAAATTG
18618230 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
18618295 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
* *
18618346 TATTGAGTCAAAAAATTTTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
18618411 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
* *
18618462 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATGTAAAATTATTATTTGT
1 TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
* *
18618527 T-GATACCAGTCAAAACATTTTTCCAAATCTAACATTAGGTTAATGT
66 TAG-TACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGT
18618573 TAGGGTTTTT
Statistics
Matches: 218, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
115 1 0.00
116 217 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.39
Consensus pattern (116 bp):
TATTAAGTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
Found at i:18618665 original size:59 final size:58
Alignment explanation
Indices: 18618589--18618982 Score: 583
Period size: 59 Copynumber: 6.7 Consensus size: 58
18618579 TTTTAAGTTA
* * *
18618589 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGG-TTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT
*
18618648 AGGGGTTAGGGGTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT
1 A-GGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT
* * *
18618707 AGGTTTAGGGTTTATAATTAATTTAGGTTAGGAGTTAGGATTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAATTTAGGTTAGG-GTTAGGGTTTTTAATTAAATTAGGTT
* * *
18618766 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT
* * * *
18618824 AGGGGTTAAGGTTTTTAATTAAATTAAGTTAGGGTTAGGG-TTTTAATTAAATTAGATT
1 A-GGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT
*
18618882 AGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAATTTAGGTTA-GGGTTAGGGTTTTTAATTAAATTAGGTT
*
18618941 AGGGTTAGGGTTTTTAATTGATTTAGGTTAGGGTTTAGGGTT
1 AGGGTTAGGGTTTTTAATTAATTTAGGTTAGGG-TTAGGGTT
18618983 AAATTAGGTT
Statistics
Matches: 303, Mismatches: 26, Indels: 12
0.89 0.08 0.04
Matches are distributed among these distances:
57 25 0.08
58 80 0.26
59 195 0.64
60 3 0.01
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.45
Consensus pattern (58 bp):
AGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:18618696 original size:88 final size:88
Alignment explanation
Indices: 18618589--18618982 Score: 664
Period size: 88 Copynumber: 4.5 Consensus size: 88
18618579 TTTTAAGTTA
18618589 AGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGT
* *
18618654 TAGGGGTTTTAATTAATTTAGGTT
65 TAGGGTTTTTAATTAAATTAGGTT
* * *
18618678 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTTAGGGTTTATAATTAATTTAGGTTAGGAGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGTT
*
18618743 AGGATTTTTAATTAAATTAGGTT
66 AGGGTTTTTAATTAAATTAGGTT
18618766 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGTT
* *
18618831 AAGGTTTTTAATTAAATTAAGTT
66 AGGGTTTTTAATTAAATTAGGTT
*
18618854 AGGGTTAGGG-TTTTAATTAAATTAGATTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGTT
18618918 AGGGTTTTTAATTAAATTAGGTT
66 AGGGTTTTTAATTAAATTAGGTT
* *
18618941 AGGGTTAGGGTTTTTAATTGATTTAGGTTAGGGTTTAGGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTT
18618983 AAATTAGGTT
Statistics
Matches: 285, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
87 84 0.29
88 189 0.66
89 12 0.04
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.45
Consensus pattern (88 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGTT
AGGGTTTTTAATTAAATTAGGTT
Found at i:18618998 original size:29 final size:29
Alignment explanation
Indices: 18618589--18618982 Score: 574
Period size: 29 Copynumber: 13.4 Consensus size: 29
18618579 TTTTAAGTTA
18618589 AGGGTTTAGGGTTTTTAATTAAATTAGGTT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTT
* *
18618619 AGGGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
18618648 AGGGGTTAGGGGTTTTAATTAATTTAGGTT
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTT
18618678 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* * *
18618707 AGGTTTAGGGTTTATAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
18618736 AGGAGTTAGGATTTTTAATTAAATTAGGTT
1 AGG-GTTAGGGTTTTTAATTAAATTAGGTT
18618766 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
18618795 AGGGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
18618824 AGGGGTTAAGGTTTTTAATTAAATTAAGTT
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTT
*
18618854 AGGGTTAGGG-TTTTAATTAAATTAGATT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
18618882 AGGGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
18618911 AGGGGTTAGGGTTTTTAATTAAATTAGGTT
1 A-GGGTTAGGGTTTTTAATTAAATTAGGTT
* *
18618941 AGGGTTAGGGTTTTTAATTGATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
18618970 AGGGTTTAGGGTT
1 AGGG-TTAGGGTT
18618983 AAATTAGGTT
Statistics
Matches: 328, Mismatches: 30, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
28 26 0.08
29 186 0.57
30 116 0.35
ACGTcount: A:0.27, C:0.00, G:0.29, T:0.45
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:18619096 original size:35 final size:35
Alignment explanation
Indices: 18618998--18619103 Score: 92
Period size: 35 Copynumber: 3.0 Consensus size: 35
18618988 AGGTTAGGGT
18618998 TTTTATTACATCAAATAAACTTCTATTTTATTACA
1 TTTTATTACATCAAATAAACTTCTATTTTATTACA
*** * * * *
18619033 TCAAATAATATCAAA-ATAAC-TCGAATTTT-TTATTA
1 TTTTATTACATCAAATA-AACTTC-TATTTTATTA-CA
*
18619068 TTTTATTACATCAAATAAACTTCTATTTTGTTACA
1 TTTTATTACATCAAATAAACTTCTATTTTATTACA
18619103 T
1 T
18619104 CAAATAAACT
Statistics
Matches: 51, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
34 6 0.12
35 39 0.76
36 6 0.12
ACGTcount: A:0.39, C:0.13, G:0.02, T:0.46
Consensus pattern (35 bp):
TTTTATTACATCAAATAAACTTCTATTTTATTACA
Found at i:18619101 original size:25 final size:25
Alignment explanation
Indices: 18619066--18619135 Score: 131
Period size: 25 Copynumber: 2.8 Consensus size: 25
18619056 AATTTTTTAT
18619066 TATTTTATTACATCAAATAAACTTC
1 TATTTTATTACATCAAATAAACTTC
*
18619091 TATTTTGTTACATCAAATAAACTTC
1 TATTTTATTACATCAAATAAACTTC
18619116 TATTTTATTACATCAAATAA
1 TATTTTATTACATCAAATAA
18619136 TATCAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.40, C:0.14, G:0.01, T:0.44
Consensus pattern (25 bp):
TATTTTATTACATCAAATAAACTTC
Found at i:18620292 original size:7 final size:7
Alignment explanation
Indices: 18620282--18620306 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18620272 TTATATACAT
18620282 AATACTA
1 AATACTA
18620289 AATACTA
1 AATACTA
18620296 AATACTA
1 AATACTA
18620303 AATA
1 AATA
18620307 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:18621479 original size:22 final size:22
Alignment explanation
Indices: 18621454--18621509 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
18621444 AAATATGGAT
18621454 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
18621476 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
18621498 TTGAGAGGAATT
1 TTGAGA-GAATT
18621510 GAGAGGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 28 0.85
23 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:18621526 original size:12 final size:11
Alignment explanation
Indices: 18621470--18621526 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
18621460 GAATTTTGGA
18621470 AGGAAATTGAG
1 AGGAAATTGAG
*
18621481 A-GAATTTTG-G
1 AGGAA-ATTGAG
18621491 AAGGAAATTGAG
1 -AGGAAATTGAG
18621503 AGG-AATTGAG
1 AGGAAATTGAG
18621513 AGGAAATATGAG
1 AGGAAAT-TGAG
18621525 AG
1 AG
18621527 AGGATTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 14 0.37
11 14 0.37
12 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:18622683 original size:11 final size:11
Alignment explanation
Indices: 18622667--18622704 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
18622657 TATTTTTTAA
18622667 TTTTAAAATAT
1 TTTTAAAATAT
*
18622678 TTTTAAAATAC
1 TTTTAAAATAT
18622689 TTTTAAAATACT
1 TTTTAAAATA-T
18622701 TTTT
1 TTTT
18622705 TTTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:18628828 original size:19 final size:19
Alignment explanation
Indices: 18628804--18628857 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
18628794 AATCTTCAAG
18628804 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
18628823 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
18628842 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
18628858 AGATATGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:18628883 original size:22 final size:22
Alignment explanation
Indices: 18628804--18628880 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 22
18628794 AATCTTCAAG
18628804 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
18628823 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
18628842 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
18628864 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
18628881 GATTTAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 32 0.62
22 8 0.15
23 12 0.23
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:18629109 original size:23 final size:23
Alignment explanation
Indices: 18629065--18629109 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
18629055 TCTTATTTTG
* *
18629065 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTAATTTA
**
18629088 TTGATTTGTATATTGTTAATTT
1 TTGATTTGTATATAATTAATTT
18629110 TAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTAATTTA
Found at i:18630924 original size:23 final size:23
Alignment explanation
Indices: 18630890--18630933 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
18630880 AAGTATGTAT
18630890 ATATATTAATTACAAATGTATAC
1 ATATATTAATTACAAATGTATAC
* *
18630913 ATATATTTATTACACATGTAT
1 ATATATTAATTACAAATGTAT
18630934 TTATAATTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (23 bp):
ATATATTAATTACAAATGTATAC
Found at i:18632793 original size:3 final size:3
Alignment explanation
Indices: 18632778--18632827 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
18632768 TAAACCTTAG
* * * *
18632778 ATT ATT TTT ATT ATT ACT ATT ATT ATT ATT ATT ATT TTT ATT ATC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18632826 AT
1 AT
18632828 CTTCATTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18644623 original size:44 final size:44
Alignment explanation
Indices: 18644518--18644717 Score: 145
Period size: 44 Copynumber: 4.4 Consensus size: 44
18644508 TAAATCAATA
* * *
18644518 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGGTCGGTTACAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAATT-AAGG-C---AACAAACC
* *
18644567 TTATCTCCCTGAAGTTGCAGTGGGGCAAATTAAGGCCACAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAGGCAACAAACC
* * ** * *
18644611 TTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAA-GTAACAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAAT-TAAGGCAACAAACC
* * * * **
18644655 TTATC-CCTGTGAAGTTGCAGTGGGGCAAGTTAAAG-ATACAAGTC
1 TTATCTCC-CTGAAGTTGCAGTGGAGCAAATTAAGGCA-ACAAACC
*
18644699 TTATCTCCTTGAAGTTGCA
1 TTATCTCCCTGAAGTTGCA
18644718 ACGAAGCAGA
Statistics
Matches: 125, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
43 4 0.03
44 83 0.66
45 4 0.03
47 1 0.01
48 4 0.03
49 29 0.23
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAGGCAACAAACC
Found at i:18644659 original size:137 final size:134
Alignment explanation
Indices: 18644335--18644677 Score: 309
Period size: 137 Copynumber: 2.5 Consensus size: 134
18644325 CATGGCGAAT
* * * *
18644335 CTTATCTCCCTAAAGTTGCAGTGGAGCA-GACTGAAGATAACAAATCTTATTTCCCTAAAGTTGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTC-GAAG-TAACAAA-CTTATCTCCCTGAAGTTGC
* * * *
18644399 AGTGGAACAGATTGAAGCTATAGATTACAGATCTCATCTCTCTGAAGTTGCAGTAGAGTAGATCA
63 AGTGGAACAGATTGAAGC-ATAGATTACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAAATCA
*
18644464 TATCAAAC
127 TAACAAAC
* * ** *
18644472 CTTACCTCCCTGAAGATGCAGTGGAGCAGGTTAAAATAAATCAATA-TTATCTCCCTGAAGTTGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTCGAAGT-AA-CAA-ACTTATCTCCCTGAAGTTGC
* * * * * * * *
18644536 AGTGGAGCAGATTGAAG-GTCGGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGGGCAAATTA-
63 AGTGGAACAGATTGAAGCATAGATTACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAAATCAT
18644599 AGGCCACAAAC
128 A----ACAAAC
* * *
18644610 CTTATCTCTCTGAAGTTGCAGTAGAGCAGGTCGAAGTAACAAACCTTATC-CCTGTGAAGTTGCA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTCGAAGTAACAAA-CTTATCTCC-CTGAAGTTGCA
18644674 GTGG
64 GTGG
18644678 GGCAAGTTAA
Statistics
Matches: 165, Mismatches: 30, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
134 1 0.01
135 36 0.22
136 6 0.04
137 82 0.50
138 39 0.24
139 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (134 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTCGAAGTAACAAACTTATCTCCCTGAAGTTGCAGT
GGAACAGATTGAAGCATAGATTACAAATCTCATCTCCCTGAAGTTGCAGTAGAGCAAATCATAAC
AAAC
Found at i:18644837 original size:182 final size:180
Alignment explanation
Indices: 18644332--18644856 Score: 523
Period size: 182 Copynumber: 2.9 Consensus size: 180
18644322 CATCATGGCG
* *
18644332 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAGATAACAAATCTTATTTCCCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTT
* * * *
18644397 GCAGTGGAACAGATTGAAGCTATAGATTACAGATCTCATCTCTCTGAAGTTGCAGTAGAGTAGAT
66 GCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
* *
18644462 CATATCAAACCTTACCTCCC-TGAAGATGCAGTGGAGCAGGTTAAAATAAATC
131 CATATCAAACCTTA--TCCCTTGAAGTTGCAGTGGAGCAAGTTAAAAT-AATC
* * * * * *
18644514 AATATTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGGTCGGTTACAAATCTTATCTCCCTGA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT-AG---CAAATCTTATTTCCCTAA
** * * * *
18644579 AGTTGCAGTGGGGCAAATTAAGGCCA-CAA--AC----CTTATCTCTCTGAAGTTGCAGTAGAGC
62 AGTTGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGC
* * *
18644637 AGGTCGAAGTAACAAACCTTATCCCTGTGAAGTTGCAGTGGGGCAAGTTAAAGAT-A-C
127 AGATC--A-TATCAAACCTTATCCCT-TGAAGTTGCAGTGGAGCAAGTTAAA-ATAATC
* ** * * * * *
18644694 AAGTCTTATCTCCTTGAAGTTGCAACGAAGCAGACTGGAGATAGCGAATCTTATTTTCGTAAAGT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGT
* *
18644759 TGCTGTGAAACAGATTAAAGCTATAAATTACAGATCTTATCAT-TCTGAAGTTGCAGTAGAGCAG
65 TGCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATC-TCTCTGAAGTTGCAGTAGAGCAG
*
18644823 ATCATATCCAAACCTTATCTCCTTAAAGTTGCAG
129 ATCATAT-CAAACCTTATC-CCTTGAAGTTGCAG
18644857 CAGGTTAAAG
Statistics
Matches: 274, Mismatches: 48, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
177 32 0.12
178 2 0.01
179 29 0.11
180 10 0.04
181 35 0.13
182 92 0.34
183 7 0.03
184 29 0.11
185 2 0.01
186 36 0.13
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (180 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTAAAGTT
GCAGTGGAACAGATTAAAGCTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT
CATATCAAACCTTATCCCTTGAAGTTGCAGTGGAGCAAGTTAAAATAATC
Found at i:18646474 original size:23 final size:23
Alignment explanation
Indices: 18646448--18646502 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
18646438 TTATTTACTT
18646448 ATTATTGTTATATTATTA-TATTA
1 ATTATT-TTATATTATTATTATTA
*
18646471 ATTAGTTTTGTATTATTATTATTA
1 ATTA-TTTTATATTATTATTATTA
*
18646495 TTTATTTT
1 ATTATTTT
18646503 TCTAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (23 bp):
ATTATTTTATATTATTATTATTA
Found at i:18650254 original size:40 final size:40
Alignment explanation
Indices: 18650199--18650279 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
18650189 ATTCGTATAT
*
18650199 TGATCCAATTATTATTCTTTCTTCTTTTGAAAGGAATTAC
1 TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
18650239 TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
1 TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
18650279 T
1 T
18650280 ATGATTCTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (40 bp):
TGATCCAATTATTATTCTTTCCTCTTTTGAAAGGAATTAC
Found at i:18651814 original size:13 final size:13
Alignment explanation
Indices: 18651798--18651824 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18651788 CTGAAAACTC
18651798 ATGCCATATTCAT
1 ATGCCATATTCAT
18651811 ATGCCATATTCAT
1 ATGCCATATTCAT
18651824 A
1 A
18651825 CTTAGTCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (13 bp):
ATGCCATATTCAT
Found at i:18652089 original size:25 final size:25
Alignment explanation
Indices: 18652060--18652114 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
18652050 TTGTTTGATT
18652060 AATATTAATATTATGATTAATTAAA
1 AATATTAATATTATGATTAATTAAA
* *
18652085 AATATTGATATTATGATTAATTAGA
1 AATATTAATATTATGATTAATTAAA
18652110 AATAT
1 AATAT
18652115 ATGAATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (25 bp):
AATATTAATATTATGATTAATTAAA
Found at i:18656866 original size:15 final size:16
Alignment explanation
Indices: 18656831--18656873 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
18656821 ATATTGCGAC
*
18656831 AAATCATAAAAAGATT
1 AAATAATAAAAAGATT
*
18656847 TAATAATAAAAA-ATT
1 AAATAATAAAAAGATT
18656862 AAATAACTAAAA
1 AAATAA-TAAAA
18656874 TAAATGAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATAATAAAAAGATT
Found at i:18661556 original size:16 final size:15
Alignment explanation
Indices: 18661535--18661564 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
18661525 TGTGCCGAGT
18661535 TTTGATAATATATTGA
1 TTTGATAATA-ATTGA
18661551 TTTGATAATAATTG
1 TTTGATAATAATTG
18661565 TATATGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (15 bp):
TTTGATAATAATTGA
Found at i:18667284 original size:26 final size:26
Alignment explanation
Indices: 18667240--18667297 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
18667230 TAGATACTAT
*
18667240 ATTTTTAGTTTTTTTATTTAATTTTA
1 ATTTTTAGTTTTTTAATTTAATTTTA
**
18667266 ATTTTTA-TTTGTTTAATTTCTTTTTA
1 ATTTTTAGTTT-TTTAATTTAATTTTA
18667292 ATTTTT
1 ATTTTT
18667298 TAGGTTGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (26 bp):
ATTTTTAGTTTTTTAATTTAATTTTA
Found at i:18669369 original size:26 final size:26
Alignment explanation
Indices: 18669339--18669391 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
18669329 TTAGTAGTTC
*
18669339 TATGCTTTGAGAATTTTTAAAGTAAA
1 TATGCTTTGAGAATTTTTAAAGCAAA
18669365 TATGCTTTGAGAATTTTTAAAGCAAA
1 TATGCTTTGAGAATTTTTAAAGCAAA
18669391 T
1 T
18669392 CAGTATTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (26 bp):
TATGCTTTGAGAATTTTTAAAGCAAA
Found at i:18676183 original size:21 final size:20
Alignment explanation
Indices: 18676150--18676189 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
18676140 CTAATCTGAT
*
18676150 CAATAGAAAATTTTAATTTA
1 CAATAGAAAATTTGAATTTA
*
18676170 CAATATGATAATTTGAATTT
1 CAATA-GAAAATTTGAATTT
18676190 TGTTATAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (20 bp):
CAATAGAAAATTTGAATTTA
Found at i:18676799 original size:22 final size:21
Alignment explanation
Indices: 18676774--18676814 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18676764 ACTTTTTATA
*
18676774 TATCATAATAATTAAAAATATT
1 TATCA-AATAAATAAAAATATT
*
18676796 TATCAATTAAATAAAAATA
1 TATCAAATAAATAAAAATA
18676815 AATTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
TATCAAATAAATAAAAATATT
Found at i:18679088 original size:15 final size:17
Alignment explanation
Indices: 18679068--18679100 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
18679058 CAGAATGAAT
18679068 AAAAATA-T-AGAAATG
1 AAAAATATTCAGAAATG
18679083 AAAAATATTCAGAAATG
1 AAAAATATTCAGAAATG
18679100 A
1 A
18679101 TTATGGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 1 0.06
17 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAAATATTCAGAAATG
Found at i:18684628 original size:24 final size:25
Alignment explanation
Indices: 18684580--18684638 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
18684570 TATATATAAT
*
18684580 ATATATTTTTGATTAAAAATAAAAA
1 ATATATATTTGATTAAAAATAAAAA
18684605 ATATATATTTGATTAAAAAT-AAAA
1 ATATATATTTGATTAAAAATAAAAA
18684629 ATATATATTT
1 ATATATATTT
18684639 AATATATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 14 0.42
25 19 0.58
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (25 bp):
ATATATATTTGATTAAAAATAAAAA
Found at i:18687730 original size:30 final size:29
Alignment explanation
Indices: 18687628--18687741 Score: 126
Period size: 28 Copynumber: 4.0 Consensus size: 29
18687618 TGTCTTGTTT
* **
18687628 AGAGGTTCGCCACTCAGGCGTTCCTTTA-
1 AGAGGTTTGCCACAAAGGCGTTCCTTTAC
18687656 AGAGGTTTGCCACAAAGGCGTTCCTTT-C
1 AGAGGTTTGCCACAAAGGCGTTCCTTTAC
*
18687684 AGAGGTTTACCACAAAGGCGTTCCTTTAAC
1 AGAGGTTTGCCACAAAGGCGTTCCTTT-AC
* * *
18687714 AGAGTTTTGTCGCAAAGGC-TATCCTTTA
1 AGAGGTTTGCCACAAAGGCGT-TCCTTTA
18687742 ATTGAGTTTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
28 50 0.68
29 2 0.03
30 22 0.30
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (29 bp):
AGAGGTTTGCCACAAAGGCGTTCCTTTAC
Found at i:18694877 original size:13 final size:13
Alignment explanation
Indices: 18694859--18694883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18694849 AGTTCTTTAT
18694859 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
18694872 TGCTTTTGAGAA
1 TGCTTTTGAGAA
18694884 ATTTGAGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:18695484 original size:22 final size:21
Alignment explanation
Indices: 18695459--18695502 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
18695449 AAGCATATGA
*
18695459 AAATGATTTGGTTATATTCAAT
1 AAATGATTTGGTTA-ATACAAT
18695481 AAATGATTTGGTTAATACAAT
1 AAATGATTTGGTTAATACAAT
18695502 A
1 A
18695503 CTTATATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (21 bp):
AAATGATTTGGTTAATACAAT
Found at i:18699399 original size:25 final size:25
Alignment explanation
Indices: 18699337--18699412 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
18699327 GTACATATAT
* *
18699337 GCTCATACGAGTTGAATAACAGTAA
1 GCTCATACAAGCTGAATAACAGTAA
* * *
18699362 GCTCCTTCTAGCTGAATAACAGTAA
1 GCTCATACAAGCTGAATAACAGTAA
* *
18699387 GCTCATACAAGCTGAGTATCAGTAA
1 GCTCATACAAGCTGAATAACAGTAA
18699412 G
1 G
18699413 TTTATAAGAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (25 bp):
GCTCATACAAGCTGAATAACAGTAA
Found at i:18702839 original size:13 final size:13
Alignment explanation
Indices: 18702823--18702847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18702813 TAACCACTTC
18702823 AATTAATTAATTT
1 AATTAATTAATTT
18702836 AATTAATTAATT
1 AATTAATTAATT
18702848 AAAACCCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTAATTAATTT
Found at i:18704126 original size:29 final size:29
Alignment explanation
Indices: 18704063--18704127 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
18704053 ATTTCCTTCT
* *
18704063 TTCCTTTCCAAAGGTTTGCCACAAAGGCG
1 TTCCTTTCCAAAAGTTTGCCACAAAGGCA
*
18704092 TACCTTTCCAAAAGTTT-CCACAAAGGCAA
1 TTCCTTTCCAAAAGTTTGCCACAAAGGC-A
18704121 TTCCTTT
1 TTCCTTT
18704128 ACATAAATAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (29 bp):
TTCCTTTCCAAAAGTTTGCCACAAAGGCA
Found at i:18713393 original size:11 final size:11
Alignment explanation
Indices: 18713357--18713400 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
18713347 CTTTAATTAG
*
18713357 ATAAAATATTA
1 ATAAAATAATA
18713368 ATAAATATCATATA
1 ATAAA-AT-A-ATA
18713382 ATAAAATAATA
1 ATAAAATAATA
18713393 ATAAAATA
1 ATAAAATA
18713401 TTCAACCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
11 16 0.55
12 3 0.10
13 3 0.10
14 7 0.24
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:18719992 original size:27 final size:27
Alignment explanation
Indices: 18719969--18720022 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
18719959 CCCTCGCAAG
18719969 CTGCTGCTT-TCCCTTAGCCATCGCACA
1 CTGCTGCTTGTCCC-TAGCCATCGCACA
*
18719996 CTGCTTCTTGTCCCTAGCCCAT-GCACA
1 CTGCTGCTTGTCCCTAG-CCATCGCACA
18720023 TCCCTTGCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 16 0.67
28 8 0.33
ACGTcount: A:0.15, C:0.41, G:0.15, T:0.30
Consensus pattern (27 bp):
CTGCTGCTTGTCCCTAGCCATCGCACA
Found at i:18724496 original size:14 final size:14
Alignment explanation
Indices: 18724477--18724517 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
18724467 GATGCTCCAG
18724477 ACGTCATCACGGGT
1 ACGTCATCACGGGT
*
18724491 ACGTCATCACTGGT
1 ACGTCATCACGGGT
*
18724505 ACTTCATCACGGG
1 ACGTCATCACGGG
18724518 ACTGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (14 bp):
ACGTCATCACGGGT
Found at i:18755190 original size:19 final size:18
Alignment explanation
Indices: 18755166--18755224 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
18755156 GAAGTAAATA
*
18755166 TTAATTTTTTTTGGCATTT
1 TTAATTTTTTTT-GAATTT
*
18755185 TTAATTTCTTTTGAATTT
1 TTAATTTTTTTTGAATTT
* *
18755203 TTCATTTTTATT--ATTT
1 TTAATTTTTTTTGAATTT
18755219 TTAATT
1 TTAATT
18755225 ATATGTTGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.26
18 14 0.41
19 11 0.32
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.69
Consensus pattern (18 bp):
TTAATTTTTTTTGAATTT
Found at i:18763279 original size:14 final size:14
Alignment explanation
Indices: 18763260--18763287 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18763250 ATGACATTTT
18763260 GACATTTAAAAATC
1 GACATTTAAAAATC
18763274 GACATTTAAAAATC
1 GACATTTAAAAATC
18763288 AATAAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
GACATTTAAAAATC
Found at i:18766005 original size:19 final size:19
Alignment explanation
Indices: 18765970--18766042 Score: 55
Period size: 19 Copynumber: 3.9 Consensus size: 19
18765960 ATTCAATTTA
18765970 AAATAAA-TAT-TTA-ATT
1 AAATAAATTATATTAGATT
18765986 AAATAAATTATATTAGATT
1 AAATAAATTATATTAGATT
* * * * *
18766005 ATATGAATAATATTTTGTTTT
1 AAATAAATTATA-TTAG-ATT
18766026 AAATAAATTATA-TAGAT
1 AAATAAATTATATTAGAT
18766043 ATTTCATTCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 7 0.17
17 3 0.07
18 4 0.10
19 14 0.33
20 3 0.07
21 11 0.26
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
AAATAAATTATATTAGATT
Found at i:18766155 original size:23 final size:23
Alignment explanation
Indices: 18766120--18766166 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
18766110 TACACAATTT
18766120 ATCTATTTCATTTAACTTAAAGA
1 ATCTATTTCATTTAACTTAAAGA
* * *
18766143 ATCTTTTTTATTTAAGTTAAAGA
1 ATCTATTTCATTTAACTTAAAGA
18766166 A
1 A
18766167 ATTATCACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (23 bp):
ATCTATTTCATTTAACTTAAAGA
Found at i:18766294 original size:173 final size:169
Alignment explanation
Indices: 18766068--18766409 Score: 486
Period size: 173 Copynumber: 2.0 Consensus size: 169
18766058 AGAAATTTAA
*
18766068 AAAAAAAGATTAATACTTAATTAAATAAATCAATTAATCAATTACACAATTTATCTATTTCATTT
1 AAAAAAAGATAAATACTTAATTAAATAAATCAATTAATCAATTACACAATTTATCTATTTCATTT
* * *
18766133 AACTTAAAGAATCTTTTTTATTTAAGTTAAAGAAATTATCACATTTAAAAAACAAGTATGTTTTT
66 AACATAAAGAA--TTTTTTATTTAACTTAAAGAAATTATCACATAT-AAAAA-AAGTATGTTTTT
18766198 CATATTAGATCAATTATCTATTCAATAAAATTAAGTGTTATTT
127 CATATTAGATCAATTATCTATTCAATAAAATTAAGTGTTATTT
* * * * * * * *
18766241 AAAAATAGATAAATATTTAATTAAATATATTAATTAATCTATTAGATAATTTATCTATTTGATTT
1 AAAAAAAGATAAATACTTAATTAAATAAATCAATTAATCAATTACACAATTTATCTATTTCATTT
* * *
18766306 AACATAAATAATTTTTTATTTAACTTAAAGAAATTATCACATATAAAAAAAGTTTTTTTTTCATA
66 AACATAAAGAATTTTTTATTTAACTTAAAGAAATTATCACATATAAAAAAAGTATGTTTTTCATA
* * *
18766371 TTAGATCAATTTTCTATTCAATAAAATTAATTTTTATTT
131 TTAGATCAATTATCTATTCAATAAAATTAAGTGTTATTT
18766410 TCAGATTACT
Statistics
Matches: 151, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
169 50 0.33
170 5 0.03
171 31 0.21
173 65 0.43
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (169 bp):
AAAAAAAGATAAATACTTAATTAAATAAATCAATTAATCAATTACACAATTTATCTATTTCATTT
AACATAAAGAATTTTTTATTTAACTTAAAGAAATTATCACATATAAAAAAAGTATGTTTTTCATA
TTAGATCAATTATCTATTCAATAAAATTAAGTGTTATTT
Found at i:18766569 original size:19 final size:19
Alignment explanation
Indices: 18766541--18766582 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 19
18766531 AAAGTAGAAC
18766541 AAAAATAAATACAAA-ATTA
1 AAAAATAAAT-CAAATATTA
18766560 TAAAAA-AAATCAAATATTA
1 -AAAAATAAATCAAATATTA
18766579 AAAA
1 AAAA
18766583 TTTTACTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAATAAATCAAATATTA
Found at i:18778550 original size:24 final size:24
Alignment explanation
Indices: 18778437--18778551 Score: 88
Period size: 24 Copynumber: 4.8 Consensus size: 24
18778427 CTCATTTACG
* * * *
18778437 TTGTGGCCAAGCGACTCAATATCT
1 TTGTGGACAAGCCACTCAATAGCA
* ** * **
18778461 TTCTGGTTAAGCCACTCATTAGTG
1 TTGTGGACAAGCCACTCAATAGCA
* *
18778485 TTGTGGACAAGCCACT-TATAGCG
1 TTGTGGACAAGCCACTCAATAGCA
* *
18778508 TTGTGGACATGCCACTCAATATCA
1 TTGTGGACAAGCCACTCAATAGCA
*
18778532 TTGTGGACAAGTCACTCAAT
1 TTGTGGACAAGCCACTCAAT
18778552 TTTGGAGTAA
Statistics
Matches: 70, Mismatches: 20, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
23 19 0.27
24 51 0.73
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (24 bp):
TTGTGGACAAGCCACTCAATAGCA
Found at i:18778701 original size:42 final size:42
Alignment explanation
Indices: 18778642--18778750 Score: 155
Period size: 42 Copynumber: 2.6 Consensus size: 42
18778632 TATCAGTCGA
* *
18778642 CATGCTTAACATGCAAATCAAATCTAAGATCAACATATTTCG
1 CATGCTTAACATGCAAATCAAATATAAGATCAACATAGTTCG
* * * * *
18778684 CATGCTTAACATGCAAATCAAATATCAGTTTATCATAGTTGG
1 CATGCTTAACATGCAAATCAAATATAAGATCAACATAGTTCG
18778726 CATGCTTAACATGCAAATCAAATAT
1 CATGCTTAACATGCAAATCAAATAT
18778751 TAGTTAATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.30
Consensus pattern (42 bp):
CATGCTTAACATGCAAATCAAATATAAGATCAACATAGTTCG
Found at i:18788681 original size:127 final size:126
Alignment explanation
Indices: 18788442--18788692 Score: 367
Period size: 127 Copynumber: 2.0 Consensus size: 126
18788432 AAAGTATTGG
* *** * *
18788442 CATAGTGTTGGACAAAGCCGACTCTTATTCACGTGTTGCCTTAGGCATGCATATCCCTACCCTTA
1 CATAATGTTGGACAAAGCCGACTCTTATTCAAACGTTGCCTTAGGCATGCATATCCCGACCCATA
* * * *
18788507 TACAAATAGTTGGACAAAGCGTATGTAGGCAAGTCTATCCCAACACTTAGGAAAGTGTCGA
66 AACAAAGAGTTAGACAAAGCGTATGTACGCAAGTCTATCCCAACACTTAGGAAAGTGTCGA
* *
18788568 CATAATGTTGGACGAAAGCCGACTCTTATTTAAACGTTGCCTTAGGCATGCATATCTCGACCCAT
1 CATAATGTTGGAC-AAAGCCGACTCTTATTCAAACGTTGCCTTAGGCATGCATATCCCGACCCAT
* *
18788633 AAACAAAGAGTTAGCCAAAGCGTATGTCCGCAAGTCTATCCCAACACTTAGGAAAGTGTC
65 AAACAAAGAGTTAGACAAAGCGTATGTACGCAAGTCTATCCCAACACTTAGGAAAGTGTC
18788693 ATCTTAGAAT
Statistics
Matches: 110, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
126 12 0.11
127 98 0.89
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.26
Consensus pattern (126 bp):
CATAATGTTGGACAAAGCCGACTCTTATTCAAACGTTGCCTTAGGCATGCATATCCCGACCCATA
AACAAAGAGTTAGACAAAGCGTATGTACGCAAGTCTATCCCAACACTTAGGAAAGTGTCGA
Found at i:18790351 original size:43 final size:44
Alignment explanation
Indices: 18790286--18790374 Score: 153
Period size: 43 Copynumber: 2.0 Consensus size: 44
18790276 ATGTGAGATA
18790286 GAGATAAAGAATTATTTAGGAATTGAATTCTATTGCAAAATATG
1 GAGATAAAGAATTATTTAGGAATTGAATTCTATTGCAAAATATG
* *
18790330 GAGAT-AATAATTATTTGGGAATTGAATTCTATTGCAAAATATG
1 GAGATAAAGAATTATTTAGGAATTGAATTCTATTGCAAAATATG
18790373 GA
1 GA
18790375 ATGATTGAGA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
43 38 0.88
44 5 0.12
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (44 bp):
GAGATAAAGAATTATTTAGGAATTGAATTCTATTGCAAAATATG
Found at i:18791993 original size:14 final size:14
Alignment explanation
Indices: 18791974--18792003 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
18791964 AAGGTGAGTC
18791974 TATTCGGCTCACAT
1 TATTCGGCTCACAT
18791988 TATTCGGCTCACAT
1 TATTCGGCTCACAT
18792002 TA
1 TA
18792004 GTGAATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.13, T:0.37
Consensus pattern (14 bp):
TATTCGGCTCACAT
Found at i:18802116 original size:19 final size:20
Alignment explanation
Indices: 18802092--18802130 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
18802082 GTTAGTGAAC
18802092 AAATATAAATAT-AAATAAA
1 AAATATAAATATAAAATAAA
**
18802111 AAATATTTATATAAAATAAA
1 AAATATAAATATAAAATAAA
18802131 TTACATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATATAAATATAAAATAAA
Found at i:18802129 original size:20 final size:20
Alignment explanation
Indices: 18802100--18802144 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
18802090 ACAAATATAA
18802100 ATATAAATAAA-AAATATTT
1 ATATAAATAAATAAATATTT
*
18802119 ATATAAAATAAATTACATATTT
1 ATAT-AAATAAA-TAAATATTT
18802141 ATAT
1 ATAT
18802145 TTAAAATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 4 0.18
20 7 0.32
22 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
ATATAAATAAATAAATATTT
Found at i:18802602 original size:20 final size:20
Alignment explanation
Indices: 18802577--18802625 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
18802567 AGGAGCAATT
18802577 AAATC-AATCTGATTAAAATC
1 AAATCAAAT-TGATTAAAATC
*
18802597 AAATCAAATTGATTAGAATC
1 AAATCAAATTGATTAAAATC
*
18802617 AAATAAAAT
1 AAATCAAAT
18802626 CAGGATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.55, C:0.10, G:0.06, T:0.29
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATC
Found at i:18805471 original size:85 final size:86
Alignment explanation
Indices: 18805328--18805538 Score: 247
Period size: 85 Copynumber: 2.5 Consensus size: 86
18805318 TAAGCGTCAA
* *
18805328 AATAAATCCCGAAAAAAATTAT-TT-AA-TTAAATCTTCTCATTTGGAAACAAAAACAAAATCGA
1 AATAAATCCAGAAACAAATTATATTCAATTTAAATC-TCTCATTTGGAAACAAAAACAAAATCGA
18805390 ATAAAATCTACTAAACGGCGGG
65 ATAAAATCTACTAAACGGCGGG
* * * *
18805412 AATAAATCCAGAAACAAATTATATTCAATTTTAATC-CTCGTTTGGAAACAAAATCAAAATGGAA
1 AATAAATCCAGAAACAAATTATATTCAATTTAAATCTCTCATTTGGAAACAAAAACAAAATCGAA
** *
18805476 TAAAATCTGTTAAACGGTGGG
66 TAAAATCTACTAAACGGCGGG
* * *
18805497 AATAAATCACTG-AACAGATTTTATTCAATTT-AAT-TCTCATTT
1 AATAAATC-CAGAAACAAATTATATTCAATTTAAATCTCTCATTT
18805539 TCAAAAAAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
84 29 0.27
85 70 0.64
86 4 0.04
87 6 0.06
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (86 bp):
AATAAATCCAGAAACAAATTATATTCAATTTAAATCTCTCATTTGGAAACAAAAACAAAATCGAA
TAAAATCTACTAAACGGCGGG
Found at i:18805677 original size:16 final size:17
Alignment explanation
Indices: 18805656--18805699 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
18805646 GTTAGTGAAG
18805656 AAATATAAATATAAA-T
1 AAATATAAATATAAATT
**
18805672 AAATATTTATATAAATT
1 AAATATAAATATAAATT
18805689 AAAT-TAAATAT
1 AAATATAAATAT
18805700 TTATATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATATAAATATAAATT
Found at i:18805685 original size:22 final size:22
Alignment explanation
Indices: 18805658--18805705 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
18805648 TAGTGAAGAA
18805658 ATATAAATATAAA-TAAATATTT
1 ATATAAAT-TAAATTAAATATTT
18805680 ATATAAATTAAATTAAATATTT
1 ATATAAATTAAATTAAATATTT
18805702 ATAT
1 ATAT
18805706 TTAAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAAATTAAATTAAATATTT
Found at i:18815921 original size:22 final size:21
Alignment explanation
Indices: 18815873--18815934 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 21
18815863 ATTCTTATAA
*
18815873 TTTT-AATTTTTTTATATTTT
1 TTTTAAATTTTTATATATTTT
* *
18815893 ATATAAATTTTTATATATTTT
1 TTTTAAATTTTTATATATTTT
* *
18815914 CTTTTAAAATTTTAAATATTT
1 -TTTTAAATTTTTATATATTT
18815935 ATATACTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
20 2 0.06
21 15 0.45
22 16 0.48
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTAAATTTTTATATATTTT
Done.